In Real Life animals don't really do much of anything, but in certain media and literature they can do things you don't usually see animals do and might or might not be smarter than the human characters.

Mewtwo fits this trope even more closely, being extremely intelligent, telepathic and not particularly friendly.

Following in Mewtwo's footsteps, most of the legendary Pokemon that appear in the movies are able to speak telepathically, be they psychic-type or not.

The wolves from Wolf's Rain are definitely smart and intimidating. Kiba and Tsume are also quite contemptuous of humans (Kiba tends to kill lots of them). They usually communicate telepathically, but when they take on their human disguises it's interpreted as actual speech. Many of the other animals are telepathic as well.

Mao from Darker Than Black is an animal-possessing Contractor who has lost his original body some time ago and now uses a black cat as his default form. The black cat body dies at the end of the first season, so he switches to a squirrel during the second season.

Ein of Cowboy Bebop probably qualifies, despite being a data dog and having a computer for a brain. Nonetheless, he's been known to utilize keyboards, play shogi, and hack into websites. The episode "Mushroom Samba" shows him holding a conversation with a cow, in which he is quite articulate.

JoJo's Bizarre Adventure shows us that developing a Stand gives an animal human-level intelligence. From Part 3 alone, we have the Boston Terrier Iggy (the Fool), Forever the orangutan (Strength), and Dio's pet falcon, Pet Shop (Horus).

Chi from Chi's Sweet Home, although she's pretty low on the intellect scale, essentially being a cat toddler. Other older pets are smarter.

From Axis Powers Hetalia, Cameroon's lion cub Kokolo, a Glasgow University Fine Arts graduate according to Hetaween 2011. Who designs and apparently makes his "master" a Halloween costume with his own hands, er, "paws".

One Piece: Tony Tony Chopper, once a normal reindeer, ate the Hito Hito no Mi devil fruit and became a talking animal with humanesque forms. Then he trained to become a doctor. By the time he joined the Straw Hat Pirates at age 15, he was a physician able to mix medicine, perform surgery, and thaw and resuscitate frozen people in an age where normal technology is about the level of the Renaissance. He's not a bad fighter, either.

It isn't clear how smart all of the animals from Mori No Ando are but the turtle appears to be able to read kanji and the fish can speak English.

Puella Magi Madoka Magica: Kyubey grants wishes to teenage girls so they will fight witches that threathen the locals. We see him traveling, giving advice, planning witch hunts and otherwise acting like a Mentor Mascot. In truth, he's working to prevent the universe's heat death and has the same opinion of humans that humans do of cattle.

The cat Shamisen in Haruhi Suzumiya asks how the rest of the cast know that he is really conversing with them and not making random sounds at random times that just happen to sound like language that fits in with their own speech, and generally talks philosophically (as long as he talks).

Norbert Sykes' god, Myrtle, from The Badger. Could be an imaginary friend, since only the hero ever sees her. The line "God is a badger named Myrtle!" will always be one of this contributor's favourites.

Although technically human, Beast from the various incarnations of the X-Men certainly evokes the same imagery.

Also Rex the Wonder Dog, who once nuked a T. rex, was a fully qualified intellectual long before the Fountain of Youth gave him the ability to talk. Hell, by that point he had already had a successful career as a newspaper photographer.

In the film adaptation of Watership Down the main group of rabbits are more intelligent than normal rabbits but they're still rabbits. All but two or three of them don't quite understand things like how some objects are able to sit on top of water and not sink and cars and tractors appear to be monsters that run along roads.

In The Secret Of NIMH, a group of rats and a pair of mice are scientifically enhanced to have human-level intelligence. Oddly enough, the family of one of the enhanced mice seem perfectly intelligent themselves, even though it's a rather important plot point that they were not enhanced above normal mice (it's possible the children were supposed to have inherited some of their father's intellect, but the wife is discriminated against by the rats for being a normal animal). The movie also features a crow who, while not especially smart, is capable of human-level conversation with mice, and an owl who gives life-saving advice.

Altivo the horse from The Road to El Dorado. When Miguel asks him to fetch a prybar so that he and Tulio can try to break loose, Altivo does one better and steals the keys.

The dinosaurs from The Good Dinosaur have developed human-like intelligence and the trappings of civilization; Arlo's family are subsistence farmers who grow corn and keep chicken-like birds, while Butch the Tyrannosaurus and his kin herd cattle.

Most of the animals in Rudyard Kipling's original Jungle Books are cynical about human nature. The Wild Child Mowgli naturally shares their attitude, leading to friction when he tries to return to human society.

Narnia has lots of non-divine mortal talking animals as well, who make a strong distinction between themselves and the regular, nonsentient sort of animals. Although not all of them are particularly intellectual.

Mercedes Lackey's Heralds of Valdemar series features a handful of non-humanoid creatures with humanoid-level intelligence, though most aren't any more gruff or cynical than what you'd expect of humans:

Gryphons, who are almost universally cheerful, vain, and entirely self-assured. Gryphons were created by a mage in the earliest parts of the series timeline, and as far as the gryphons are concerned, they're an improvement on sentient life as a whole.

The dyheli, deer creatures with Psychic Powers, a stong herd mentality, and the fuzzy concept of free will that you get when you mash the first two together. Probably the most powerful minds in the series; in one novel, a dyheli herd leader repeatedly displays the ability to ignore mental shields in order to get concepts across. They allow the Tayledras to ride them as equal partners.

There's also the Companions and the Firecats, although they're less cool animals and more spirits in useful form or proxies of their deity, respectively.

It still remains unclear whether Jonathan Swift meant the Houhynhyms of Gulliver's Travels to be taken seriously in their cynical, anti-human perspective. (Inverted in the Yahoos with which they share their island, who are unintelligent humans, or perhaps very humanlike apes.)

Frith and the Black Rabbit of Inlé, the rabbit gods from Watership Down.

Poul Anderson's novel Brain Wave, where Something sends the IQ's of every animal on Earth soaring, including Humankinds, resulting in The Singularity.

Einstein, a rather modified Golden Retriever, in Watchers, by Dean Koontz. He loves to read, plays a good game of Scrabble, and has fun teasing his humans.

The Bunyip in Naomi Novik's Tounges of Serpents, a race of landgators adapted to living underground who set complex traps, communicate between communities and understand the concept of trade/bribery.

Harry Potter invokes this by way of the Wolfsbane Potion, which allows werewolves who drink it to keep their mind in a human state.

The Treecats of Honor Harrington are fully sentient, have a civilization spanning most of their home world, history (via recorded memories) dating back thousands of years, and as of book 7 have started colonizing other planets.

Dinotopia is an entire island populated by this kind of character. In particular, Bix hates it when anyone calls her their Non-Human Sidekick.

Dr. Dillamond (a goat) in Wicked. Gregory Maguire's Oz is populated by numerous Funny Animals, but Dr. Dillamond is the only one who appears as a named character, and is most definitely intellectual.

Any animal bonded as a Familiar by a wizard gains a significant intelligence boost. Past middle levels, familiars get significantly smarter than the average human.

The Awaken spell can permanently turn an animal into this. Some take it well, others... less so. Since no druid wants to deal with a genius dire wolf wizard who blames them for taking it away from its pack, it's not often used.

Zig-zagged with the rabbit characters of Bunnies & Burrows. On the one hand, they have organized societies with roles like Storytellers and Seers. On the other, they're quite dim compared to humans: concepts like writing and numbers larger than four are forever beyond their grasp.

Video Games

Red XIII, aka Nanaki, from Final Fantasy VII is perhaps the prime example of this in video games. Red is especially weird; not only is he smart for an "animal", he's probably the smartest member of your party. Even weirder is when it's revealed that, adjusting for his species' lifespan, Red is a teenager, making him a sort of Teen Genius on top of being an Intellectual Animal.

Koromaru from Persona 3, who's a dog (an albino Shiba Inu, to be exact). While he can't talk, he's smarter than Junpei, capable of detecting shadows, is great with a knife, and is capable of summoning a Persona.

Boney of MOTHER 3 fits this pretty well, although he is a charming chocolate labrador as opposed to something more intimidating. Despite this, he occasionally speaks with the party (how he does this is never explained) and blends human-level intelligence with animal instincts, taking offense to an NPC suggesting his use as bait for a raging monster one moment, and dropping everything to chase after insects the next.

PSI-users can communicate with animals using telepathy, though Lucas could do this even before his powers awakened.

Repede, to the point of acting more human than dog at times. He is pretty much an expy of Blanca.

The mabari hounds from Dragon Age: Origins are described as having almost-human intelligence, and legend even tells that they're "smart enough to speak, but wise enough not to". You can recruit a mabari into your party, and he occasionally "converses" with your other party members while you wander around.

Thomas Kemper (the cat) from Penny Arcade may qualify, while he is never shown doing anything out of the ordinary it is mentioned that he has some sort of Microsoft Professional Certification and he may or may not have designed an industrial laser and possibly a time machine.

Xanther from Elven Lacryment seems to be the lead character's psychiatrist.

Blackwing the raven from The Order of the Stick has recently become this, offering advice and insight to his master, Vaarsuvius. Justified in that he's the familiar of a powerful wizard, so he's likely smarter than most humans.

The SCP Foundation has a few of these under its watch. SCP-1156 is a talking coach horse named Wellington who can somehow summon clothes onto his body. SCP-1867 is a telepathic sea slug who claims to be a ninteenth-century explorer and naturalist named Theodore Thomas Blackwood, and has a vault full of unknown-to-science specimens to back his claims. SCP-1845 is a kingdom of animals based on a feudalistic European model, led by a dynastic line of foxes, whose inhabitants can't talk, but can read, write, and make tools such as musical instruments, canoes, and rosaries.

Western Animation

Klaus, the Smith family's goldfish on American Dad!, fits this. Of course, Klaus isn't just a goldfish; he used to be an East German Olympic ski-jumper until his brainwaves were switched with that of a goldfish in the 1986 Winter Olympics (which did not exist) by the CIA to prevent him from winning the gold medal. He also has a rather overt... "fascination" with Mrs. Smith. Paging Troy McClure, line one Mr. McClure...

Many animals in Avatar: The Last Airbender, but most notably Appa, the badger moles, the dragons, and the Giant Lion Turtle. Not to mention animal spirits like Wan Shi Tong the knowledge owl.

A Batman Beyond episode was all about a gorilla being turned into this when his DNA was spliced with a human's.

Spoofed in "Guess Who's Coming To Criticize Dinner" when Homer became a food critic and was writing a review. Due to a fight couldn't turn to Lisa for help, so he started asking the family dog for advice.

The animals in Mike, Lu & Og, in contrast to the human inhabitants of the island.

GadgetHackwrench of Chip 'n Dale Rescue Rangers is one of the Funny Animal variety. She's a mouse with a demonstrably higher IQ than...well, pretty much everyone on the show, human and animal alike. However unlike most examples she never lords this over anyone (even unintentionally) and she's good-natured and kind to a (literal) fault. Usually.

Brain from Inspector Gadget displays a great deal more situational awareness and common sense than the titular character, whom he must constantly protect from harm.

Aladdin has Iago, a very witty and smart talking parrot. Abu the monkey is also smart, but can't talk.

Tracy from Filmation's Ghostbusters. Downplayed in the live-action series, though: Tracy is a genius, but only when compared to Spenser and Kong. It's more pronounced in the animated series, wherein Tracy is seen building Homemade Inventions and maintaining/repairing the Ghostbusters' gear.

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